extract_sigma_r: Extract the 'sigma_R_info' table from a data frame of...

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Extract the sigma_R_info table from a data frame of recruitment parameters

Description

Extract the sigma_R_info table from a data frame of recruitment parameters

Usage

extract_sigma_r(models = NA, model_names = NA, sigma_r_in = NA)

Arguments

models	A list of models extracted using r4ss::SS_output(). If only one model,it must be a list with one element containing the model
model_names	A vector of names, one for each model in models. This vector must be the same length as models
sigma_r_in	The input value used for sigma_R, this is also available in the list output by r4ss::SS_output() and is used to scale the results

Details

Extract the sigma_R_info table that is available in the object returned from r4ss::SS_output(). Typically, this table is determined from MLE results, but this function also offers the capability to calculate this info from the table of MCMC results as well.

Based on the non-exported function extract_sigma_R_info() in r4ss, but with a wrapper for more than one model

Value

A data frame is returned with three rows for each model in the models list and 11 columns. Rows provide summary statistics for a given group of recruitments, where the rows are additive in their inclusiveness, i.e., the data frames used to calculate rows two and three include all data used in the calculations that led to the results displayed in the first row. Columns include the following variables:

• period: Categories that specify which recruitments were included in the subset used to calculate the summary

• N_devs: The number of recruitment estimates used in the summary

• SD_of_devs: The standard deviation (sd) of the recruitment deviations.

• Var_of_devs: The variance (var) of the recruitment deviations

• mean_SE: The mean of the estimated standard error (se) of the recruitment deviations, or more precisely, the mean of the Parm_StDev column of your data

• mean_SEsquared: The mean of the squared estimates of standard error of the recruitment deviations, i.e., mean(Parm_StDev^2)

• sqrt_sum_of_components: The square root of the sum of the deviation and the standard error

• SD_of_devs_over_sigma_R: The scaled version of SD_of_devs

• sqrt_sum_over_sigma_R: The scaled version of sqrt_sum_of_components

• alternative_sigma_R: The suggested value for a new input sigma_R, which is just a repeat of the sum of components column

pacific-hake/hake-assessment documentation built on Jan. 14, 2025, 9:12 p.m.